9 Differences in microglia by sample & treatment
9.1 Total microglia states
Uniform Manifold Approximation and Projection (UMAP) visualization of 29854 microglial cells.
Each point represents a single cell, and cells are colored according to unsupervised clusters identified from transcriptomic profiles.
9.2 Total cells
Bar plot showing the number of cells assigned to each cluster.
9.3 Gene Heatmap & hierarchical cluster
Heatmap of normalized expression levels for representative marker genes across clusters, with hierarchical clustering applied to both genes and clusters, providing an overview of the molecular signatures that distinguish microglial states.
9.4 Proportions (%) of Microglial States Across Samples and Treatments
Stacked barplot of the relative abundance of each microglial Seurat-defined cluster in individual samples and compared proportions between the Aducanumab-treated and IgG control groups.
| Adu | IgG | p.overall | |
|---|---|---|---|
| N=3 | N=3 | ||
| NFkB/IEG Activated | 23.3 [22.0;23.8] | 25.9 [24.8;26.1] | 0.127 |
| Homeostatic (Activation competent) | 14.9 [14.9;15.1] | 19.6 [18.5;20.1] | 0.050 |
| DAM (Early/Intermediate) | 18.5 [17.4;19.0] | 13.9 [13.3;14.4] | 0.050 |
| Remodeling / Injury response | 12.5 [12.3;12.6] | 11.1 [11.1;11.8] | 0.268 |
| Homeostatic (canonical) | 10.6 [10.4;11.8] | 11.1 [10.2;12.6] | 0.827 |
| DAM (late) | 11.2 [9.80;12.3] | 11.8 [11.5;11.9] | 0.658 |
| Antigen presenting | 7.10 [4.30;7.10] | 2.40 [2.40;4.20] | 0.500 |
| Interferon responsive | 3.60 [3.25;3.70] | 2.70 [2.65;2.90] | 0.127 |
| Proliferating | 0.60 [0.45;0.80] | 0.50 [0.45;0.55] | 0.658 |
Values are median % of microglia in that cluster per sample, with IQR.
p.overall: Mann-Whitney p-value
9.5 Module scores
UMAP displaying the combined expression scores or the distribution of individual canonical microglial marker genes, illustrating the transcriptional features that define each cluster.
Markers from bibliography to generate the scores
| Signature | genes |
|---|---|
| AP | Cd74, B2m, Cd37, Lgals1, Rpl26, Rps19, Rps8, Rps4x, Rps15a, H2-Eb1, H2-Ab1, H2-Aa |
| CRM | Il1b, Ch25h, Padi2, Plek, Tlr2, Junb, C3ar1, Nfkbia, Trem2, Tyrobp |
| DAM | Spp1, Lipa, Apoc1, Ccl3, Fabp5, Trem2, Cxcr4, Gpnmb, Litaf, Cstb, Rps18, Rpl11, Rpl37a, Axl, Dbi |
| Homeostatic | P2ry13, P2ry12, Cx3cr1, Cst3, Ltc4s, Bin1, Maf, Frmd4a, Csf1r, C1qa, Dock8, Stab1, Sparc |
| IRM | Ifit2, Il1b, Epsti1, Eif2ak2, Bst2, Tnfsf10, Sp110, Irf1, Tap1, Adar, Cd48, Nampt |
| TIM | Klf4, Malat1, Tmx4, Jund, Btg2, Jun, Fos, Klf2 |
Red dots indicate cells with high signature scores (top 25%), while grey represents cells with lower scores
Homeostatic
DAM: Disease associated microglia
AP : Antigen Presenting (HLA/MHC class II)
IRM : Interferon-response microglia.
CRM : Cytokine-Response microglia Markers described in (Fumagalli et al. 2025)
TIM : Terminally inflammatory microglia (Millet, Ledo, and Tavazoie 2024)
9.6 Microglia states according to (Fumagalli et al. 2025)
Using AddModuleScore in the previous step, each cell received a numerical score for each signature.
Then, for each cell, the maximum score across all signatures was identified, and the corresponding label was assigned as its “dominant phenotype.” This categorical assignment was stored in the metadata under the identity class score_cluster.
| Adu | IgG | p.overall | |
|---|---|---|---|
| N=3 | N=3 | ||
| AP | 17.9 [17.0;19.2] | 15.1 [15.1;15.4] | 0.046 |
| CRM | 36.8 [35.9;38.5] | 42.6 [39.1;44.5] | 0.275 |
| DAM | 3.60 [3.25;4.20] | 3.40 [3.30;4.10] | 1.000 |
| Homeostatic | 42.0 [38.8;43.0] | 38.2 [36.5;41.2] | 0.827 |
| IRM | 0.30 [0.20;0.30] | 0.20 [0.15;0.25] | 0.637 |